chr4-111002885-C-T

Variant names:

• chr4-111002885-C-T
• rs9307358
• ENST00000681682.2:n.493+88767C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000681682.2(ENSG00000288692):​n.493+88767C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,088 control chromosomes in the GnomAD database, including 5,433 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (5433 hom., cov: 32)
• Consequence: ENSG00000288692 ENST00000681682.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 2 publications found

Genes affected

ENSG00000288692 (HGNC:):

ENSG00000309167 (HGNC:58950):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000681682.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288692	ENST00000681682.2		n.493+88767C>T		intron	N/A
	ENSG00000309167	ENST00000839195.1		n.185-560G>A		intron	N/A
	ENSG00000309167	ENST00000839196.1		n.183-560G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24926 AN: 151972 Hom.: 5406 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0636

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.0245

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.131

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.164 AC: 24994 AN: 152088 Hom.: 5433 Cov.: 32 AF XY: 0.162 AC XY: 12068 AN XY: 74364

African (AFR) AF: 0.494 AC: 20436 AN: 41400

American (AMR) AF: 0.0634 AC: 970 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3470

East Asian (EAS) AF: 0.267 AC: 1382 AN: 5168

South Asian (SAS) AF: 0.0938 AC: 452 AN: 4818

European-Finnish (FIN) AF: 0.0245 AC: 260 AN: 10602

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0163 AC: 1110 AN: 68014

Other (OTH) AF: 0.135 AC: 286 AN: 2114

Alfa AF: 0.0514 Hom.: 1483

Bravo AF: 0.182

Asia WGS AF: 0.205 AC: 713 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.45
PhyloP100		-0.10

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9307358;

hg19: chr4-111924041;